Nowadays, robust position, navigation and timing (PNT) information becomes an necessary foundation of e-navigation and requires the trials and development of a new system to improve marine navigation. Positioning estimation methods and their implementation are being investigated in the literature due to their importance in safety and national security services. In this paper, we propose a novel method for the position estimation of the vessel using both time of arrival and time difference of arrival in the automatic identification system (AIS), which leads to an alternative system for complementing the existing satellite navigation, positioning and timing services to support enavigation and made a potential backup system available. Furthermore, the performance of the proposed hybrid positioning method is evaluated, especially for the accuracy. Finally, the accuracy of the position estimation is compared to the conventional methods, and the simulation results have shown the perfect working area.